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Detailed information for vg0414551751:

Variant ID: vg0414551751 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 14551751
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.55, A: 0.44, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


TCATTGTGTACCTGCCTAAAATTTTCCCTATAAGAGTTTGGGCTGGGTAGGTACAAGTTGTAGGAGCTTTGGTGAAAATGATGATCAGCTACAACGAAAA[G/A]
TAGACACGTGTCACATGTGGGATTGAGGTGCAGATGCACCTAGGTTCATATTATCCAACTCCTATATATATATATACATATACATATACATATATATATA

Reverse complement sequence

TATATATATATGTATATGTATATGTATATATATATATAGGAGTTGGATAATATGAACCTAGGTGCATCTGCACCTCAATCCCACATGTGACACGTGTCTA[C/T]
TTTTCGTTGTAGCTGATCATCATTTTCACCAAAGCTCCTACAACTTGTACCTACCCAGCCCAAACTCTTATAGGGAAAATTTTAGGCAGGTACACAATGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.30% 39.20% 1.06% 8.51% NA
All Indica  2759 51.00% 40.20% 1.49% 7.39% NA
All Japonica  1512 60.60% 26.90% 0.20% 12.30% NA
Aus  269 1.90% 98.10% 0.00% 0.00% NA
Indica I  595 41.70% 30.80% 0.67% 26.89% NA
Indica II  465 18.50% 78.10% 3.23% 0.22% NA
Indica III  913 76.80% 21.10% 1.20% 0.88% NA
Indica Intermediate  786 47.20% 46.90% 1.40% 4.45% NA
Temperate Japonica  767 82.30% 2.60% 0.13% 14.99% NA
Tropical Japonica  504 23.60% 67.70% 0.20% 8.53% NA
Japonica Intermediate  241 68.90% 19.10% 0.41% 11.62% NA
VI/Aromatic  96 53.10% 34.40% 4.17% 8.33% NA
Intermediate  90 50.00% 43.30% 2.22% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0414551751 G -> DEL N N silent_mutation Average:14.725; most accessible tissue: Callus, score: 35.369 N N N N
vg0414551751 G -> A LOC_Os04g25180.1 upstream_gene_variant ; 3923.0bp to feature; MODIFIER silent_mutation Average:14.725; most accessible tissue: Callus, score: 35.369 N N N N
vg0414551751 G -> A LOC_Os04g25170.1 downstream_gene_variant ; 3333.0bp to feature; MODIFIER silent_mutation Average:14.725; most accessible tissue: Callus, score: 35.369 N N N N
vg0414551751 G -> A LOC_Os04g25170-LOC_Os04g25180 intergenic_region ; MODIFIER silent_mutation Average:14.725; most accessible tissue: Callus, score: 35.369 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0414551751 NA 2.42E-06 mr1121 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0414551751 NA 5.62E-06 mr1192 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0414551751 NA 1.29E-07 mr1423 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0414551751 NA 9.18E-06 mr1543 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0414551751 9.00E-07 8.96E-07 mr1736 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0414551751 NA 3.92E-06 mr1944 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0414551751 NA 2.32E-08 mr1993 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0414551751 NA 7.33E-07 mr1121_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0414551751 NA 1.39E-06 mr1248_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0414551751 NA 6.43E-06 mr1319_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0414551751 NA 2.01E-06 mr1423_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0414551751 NA 1.24E-16 mr1699_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0414551751 NA 2.70E-07 mr1733_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251